Greg,
Can I use the DAS2 server framework to write the Haploview service?
-B
--
Brian Gilman
President Panther Informatics Inc.
E-Mail: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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On Oct 28, 2008, at 2:02 PM, Gregg Helt wrote:
I'm pleased to announce I've got a DAS1 to DAS2 transformational proxy
working. I'm calling it Trellis/Ivy. Trellis is the overall DAS2
server
framework, and Ivy is the DAS1 proxy plugin. The source code is
available
via SVN at http://code.google.com/p/genomancer/ . This should
definitely be
considered a beta release, there are plenty of features that aren't
yet
implemented and I'm sure still some bugs in what is implemented.
I'm hoping a stable version of this can eventually be set up close
to or
integrated with the DAS1 registry. For current testing I've
deployed an
instance of Trellis/Ivy at genomancer.org in the Amazon EC2 cloud.
It's
hardwired to proxy for the Sanger DAS1
registry<http://www.dasregistry.org/das1/sources>.
Some example DAS2 queries and the DAS1 queries they proxy for:
All DAS1 registry sources:
http://www.dasregistry.org/das1/sources
All DAS1 registry sources --> DAS1+2 sources
http://www.genomancer.org/das2/das1_proxy/sources
DAS1 filtered sources
http://www.dasregistry.org/das1/sources?type=Chromosome&capability=types
DAS1 filtered sources --> DAS1+2 filtered sources
http://www.genomancer.org/das2/das1_proxy/sources?type=Chromosome&capability=types
Ensembl DAS1 entry points
http://www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points
Ensembl DAS1 entry points --> DAS2 segments
http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points
Uniprot DAS1 types
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types
Uniprot DAS1 types --> DAS2 types:
http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types
Uniprot DAS1 features (from UniProt DAS home page example)
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502
UniProt DAS1 features --> DAS2 features
http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502
Ensembl DAS1 features (from Ensembl DAS home page example)
http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13:31787617,31871806
Ensembl DAS1 features --> DAS2 features
http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13;overlaps=31787616:31871806
UCSC-Gencode segment/overlap/type-filtered, URL-encoded, DAS2 feature
request (copied from IGB testing):
http://www.genomancer.org/das2/das1_proxy/hgwdev-gencode.cse.ucsc.edu/cgi-bin/das/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2F21;overlaps=26014828%3A26071595;type=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2FknownGene
Basic DAS1.53 query --> DAS2.0 conversions not yet implemented:
DAS1 sequence --> DAS2 segments
DAS1 dsn --> DAS2 sources
DAS1 stylesheet --> DAS2 stylesheet
I'll post a summary of plans for these queries and other features
soon, but
I wanted to at least send out this announcement so people who are
interested
can check out the examples. Please let me know what you think.
Gregg
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